Mercurial > repos > iuc > medaka_consensus_pipeline
diff medaka_consensus.xml @ 10:1ca4ce7241fd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author | iuc |
---|---|
date | Thu, 22 Apr 2021 20:25:13 +0000 |
parents | a1b70f038b4a |
children | 8dfe8a52346f |
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--- a/medaka_consensus.xml Mon Mar 29 20:06:44 2021 +0000 +++ b/medaka_consensus.xml Thu Apr 22 20:25:13 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Assembly polishing via neural networks</description> <macros> <import>macros.xml</import> @@ -11,9 +11,6 @@ -m ${m} -b $b -o results -#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',') - -v -#end if -t \${GALAXY_SLOTS:-4} ## required -i '$i' @@ -26,14 +23,13 @@ <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> <expand macro="model"/> <expand macro="b"/> + <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Don't fill gaps in consensus with draft sequence?" checked="false" /> <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v."> <option value="consensus" selected="true">Consensus</option> <option value="probs" selected="true">Consensus probabilities</option> <option value="calls" selected="true">Calls to draft</option> - <option value="draft">Draft to consensus</option> - <option value="variants">Variants</option> - <option value="polished">Polished regions in draft coordinates</option> <option value="log">Log</option> + <option value="gaps">Gap regions in draft</option> </param> </inputs> <outputs> @@ -47,15 +43,8 @@ <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft"> <filter>'calls' in out</filter> </data> - <!-- optional with parameter -v --> - <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus"> - <filter>'draft' in out</filter> - </data> - <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants"> - <filter>'variants' in out</filter> - </data> - <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft"> - <filter>'polished' in out</filter> + <data name="out_gaps" format="bed" from_work_dir="results/consensus.fasta.gaps_in_draft_coords.bed" label="${tool.name} on ${on_string}: Gaps in draft"> + <filter>'gaps' in out</filter> </data> <!-- optional --> <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> @@ -70,13 +59,13 @@ <output name="out_consensus"> <assert_contents> <has_n_lines n="2"/> - <has_line line=">4_segment0 4:1.0-3792.0"/> + <has_line line=">4"/> <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> </assert_contents> </output> <output name="out_probs"> <assert_contents> - <has_size value="165271" delta="100"/> + <has_size value="165503" delta="100"/> </assert_contents> </output> <output name="out_calls"> @@ -86,17 +75,16 @@ </output> </test> <!-- #2 --> - <test expect_num_outputs="7"> + <test expect_num_outputs="5"> <param name="i" value="basecalls.fastq"/> <param name="d" value="assembly.fasta"/> <param name="m" value="r941_min_fast_g303"/> <param name="b" value="99"/> - <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/> + <param name="out" value="consensus,probs,calls,log,gaps"/> <output name="out_consensus"> <assert_contents> - <has_n_lines n="65"/> - <has_line line=">4 length=3792 depth=114.52x circular=true"/> - <has_line line="ATCTCTTT"/> + <has_n_lines n="2"/> + <has_line line=">4"/> <!-- Replace test --> </assert_contents> </output> <output name="out_probs"> @@ -109,27 +97,16 @@ <has_size value="343197" delta="100"/> </assert_contents> </output> - <output name="out_draft"> - <assert_contents> - <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/> - <has_line line="1409 1 0"/> - <has_line line="440 1 0"/> - <has_line line="736 1 0"/> - <has_line line="853 1 0"/> - <has_line line="350"/> - </assert_contents> - </output> - <output name="out_polished"> - <assert_contents> - <has_size value="9"/> - </assert_contents> - </output> - <output name="out_variants" file="variants.vcf.gz" decompress="true"/> <output name="out_log"> <assert_contents> <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> </assert_contents> </output> + <output name="out_gaps"> + <assert_contents> + <has_size value="0" delta="0"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[